MolNFT v1 · #124158 · protein
Sidekick-2 immunoglobulin domains 1-4, crystal form 2
5K6Y · Protein sidekick-2: “Sidekick-2 immunoglobulin domains 1-4, crystal form 2”. X-ray diffraction, 2 ligands (NAG, FUC), 9 pockets (best druggability 0.71). MolNFT v1 #124158 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5K6Y
- Type
- protein
- Length
- 739 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein sidekick-2
- UniProt
- Q6V4S5
- Ligands
- NAG, FUC
- Pockets
- 9 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein sidekick-2 | protein | 374 | 4% helix, 55% strand | Q6V4S5 |
| B | Protein sidekick-2 | protein | 365 | 4% helix, 53% strand | Q6V4S5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.71 | 0.75 | 81 | empty |
| 2 | 307 | 0.71 | 0.84 | 49 | empty |
| 3 | 647 | 0.68 | 0.77 | 50 | empty |
| 4 | 192 | 0.58 | 0.80 | 24 | empty |
| 5 | 108 | 0.52 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1359 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q6V4S5
- Elsewhere: RCSB PDB 5K6Y · PDBe 5K6Y · UniProt Q6V4S5
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